*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Xu Tan, I don't have any experience running APBS with pymol, but I use it combined with chimera (http://www.cgl.ucsf.edu/chimera/) with no trouble on an iBook G4. If you run "fink" in your Mac, which is extremely useful for the installation of other crystallographic software thanks to Bill Scott among others, you can get both apbs and pdb2pqr. Chimera installs from binaries distributed (free for academic) by the authors. The output that standalone (or web-server) pdb2pqr creates will not be useful directly to calculate your electrostatic potential: it is intended to calculate solvation energy, so it does two calculations, the second one has a dielectric constant .=. 2 for both inside and outside the protein, and is then subtracted from the first one. In order to calculate the electrostatic potential, you simply remove the second calculation and the subtraction and add this line after the first calculation: write pot dx filename this will produce a file called 'filename.dx' that is written in the OpenDx format, that can be read by Chimera (and, I presume, by Pymol as well). Other excellent software can read this file: VMD, for example In Chimera, like in VMD, you can map the electrostatic potential on the molecular surface, but you can also represent it as an 'isosurface' that will give you a good idea about the presence of dipoles, or about how the electrostatic potential extends beyond the molecular surface. I can give you more detail if you find my explanation unclear. It's really easy to do, really ;-) Good luck, Miguel En/na Xu TAN ha escrit: > > Hi all, > > Thanks for all the responses to the alternatives to GRASP question, > turned out > it is a quite provocative one ! > Based on all the responses, APBS coupled with Pymol seems to be a > popular > choice for electrostatics surface calculation. However, I installed > twice apbs > on my macintel (OSX 10.4), first just the binary and then by fink . I > can get it running > now, but however I generate the .pqr file (by pymol and by the pdb2pqr > server), there > is always this error message: " ObjectMapLoadDXFile-Error: Unable to > open file!" > Basically, when I run apbs in pymol, there is all the wild flashing > around in pymol, and > then the error message shows up. If I run apbs in command line using the > server > generated .in and .pqr files, then the below messages coming out: > > Valist_readPQR: Error parsing ATOM field! > Error while reading molecule from 11679388051.pqr > Error reading molecules! > > I tried to make sure there is a END sign in the end of .pqr. So is there > anybody who succeeded running apbs on a Mac and what is the trick ?? > > Thanks a million > > Xu Tan > University of Washington, Seattle > - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: [EMAIL PROTECTED] - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFFnWCIF6oOrDvhbQIRAmsWAJ94ndTXAyh/o0DV3RfaP3tVo/4hPACdHBDo fe1NpO2t4a+55NzYMlBnYIk= =WAMa -----END PGP SIGNATURE-----
